Historical demography
PSMC (Li & Durbin 2011) was used on consensus genomic sequence data to
characterize historical demography by examining heterozygosity densities
in 100bp sliding windows across the genome. PSMC was run twice for each
individual, once utilizing all mapped sequence data and again on data
down-sampled to 20X coverage (near the lowest coverage sample) using the
DownsampleSam tool (Picard). Results were scaled by a general mammalian
mutation rate (2.2 x 10^-9 per base pair per year; Kumar &
Subramanian 2002) and marten generation time (5 years), resulting in
distributions of effective population size (Ne) through
time. One hundred PSMC bootstrap replicates were performed and plotted
for both full-coverage and down-sampled data to confirm consistent
distributional shapes and enable comparison across individuals, as PSMC
is sensitive to variation in coverage depth (ideal coverage
>18X; Nadachowska-Brzyska et al. 2016).